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Sample summary
Input data: infant stools (BS1, BS2, BS3, and BS5) and maternal stool (MS1)
- n samples = 2086
- n taxa: genera = 487; variants = 6239
- n taxa (rarefied): genera = 453; variants = 6103
- mean read count = 1.428810^{5}, s.d. = 1.358610^{5}
Statistical methods for mixed-effects models
- Linear mixed-effects models fit with family ID as a random effect
- Effect of country determined by comparing: (i) model with country/age vs (ii) model with age alone
- Pairwise comparisons between countries (M vs I, U vs I, U vs M) corrected by FDR to control family error rate
- OPV/IPV arms from India combined in primary comparison
- Diversity in maternal samples compared by country via ANOVA with post-hoc Tukey test
Taxon abundance profile
Column
Genus-level
India - infant
Malawi - infant
UK - infant
India - maternal
Malawi - maternal
UK - maternal
RSV-level
India - infant
Malawi - infant
UK - infant
India - maternal
Malawi - maternal
UK - maternal
Alpha diversity
Column
Genus-level
India vs Malawi vs UK
p values (FDR-adjusted, 4 decimal places)
Shannon Richness
Malawi-India 0.0000 0.0000
UK-India 0.2133 0.4976
UK-Malawi 0.0322 0.0000p values, India (OPV) vs India (IPV)
Shannon Richness
India (OPV)-India (IPV) 0.4666 0.2373Maternal samples
p values, India vs Malawi vs UK
Shannon Richness
Malawi-India 0.9782 0.1271
UK-India 0.0001 0.0001
UK-Malawi 0.0029 0.0000p values, India (OPV) vs India (IPV)
Shannon Richness
1 0.6511 0.8167RSV-level
India vs Malawi vs UK
p values (FDR-adjusted, 4 decimal places)
Shannon Richness
Malawi-India 0.0000 0.0000
UK-India 0.0032 0.6661
UK-Malawi 0.3792 0.0010p values, India (OPV) vs India (IPV)
Shannon Richness
India (OPV)-India (IPV) 0.5419 0.7797Maternal samples
p values, India vs Malawi vs UK
Shannon Richness
Malawi-India 0.000 0e+00
UK-India 0.054 6e-04
UK-Malawi 0.000 0e+00p values, India (OPV) vs India (IPV)
Shannon Richness
1 0.6978 0.8935Longitudinal abundance plots
Infants - India vs UK vs Malawi
Infants - India (OPV) vs India (IPV)
Maternal samples (with genera corresponding to infant plots included)
Beta diversity
Column
Genus-level
Bray-Curtis distances (weighted)
Bray-Curtis distances (unweighted)
Turnover, paired vs random (weighted)
For week 1, distance from maternal sample plotted. For subsequent samples, distance from prior infant sample plotted.
Turnover, paired vs random (unweighted)
Longitudinal samples from a given infant more closely clustered than expected by chance in each of the three cohorts.
RSV-level
Bray-Curtis distances (weighted)
Bray-Curtis distances (unweighted)
Turnover, paired vs random (weighted)
For week 1, distance from maternal sample plotted. For subsequent samples, distance from prior infant sample plotted.
Turnover, paired vs random (unweighted)
Longitudinal samples from a given infant more closely clustered than expected by chance in each of the three cohorts.
Differential taxa
Column
Genus-level
Cross-validation accuracy, India vs Malawi vs UK
Cross-validation accuracy, India (OPV) vs India (IPV)
Pre-vaccination comparisons (main manuscript figure)
Grid of all other comparisons
Differential prevalence plots
RSV-level
Cross-validation accuracy, India (OPV) vs Malawi vs UK
Cross-validation accuracy, India (OPV) vs India (IPV)
Pre-vaccination comparisons
Grid of all other comparisons
Differential prevalence plots
Longitudinal abundance comparisons
India vs UK
Number of genera tested: 31
Number of discriminant genera (FDR p < 0.1): 25 (India = 14; UK = 11) Failed to converge: 0
India vs Malawi
Number of genera tested: 42
Number of discriminant genera (FDR p < 0.1): 29 (India = 8; Malawi = 21) Failed to converge: 0
Malawi vs UK
Number of genera tested: 44
Number of discriminant genera (FDR p < 0.1): 31 (Malawi = 22; UK = 9) Failed to converge: 0
Construct tree
Longitudinal abundance plots for major genera
